Variant report

Variant	rs2809879
Chromosome Location	chr1:242948495-242948496
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11587925	0.98[ASN][1000 genomes]
rs11590438	0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12725738	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs12745561	0.98[ASN][1000 genomes]
rs2780779	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2780780	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2780781	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2809896	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33939589	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs914950	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs914951	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430391	chr1:242307104-243280885	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv817488	chr1:242330066-243121127	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv868888	chr1:242330066-243191101	Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv549465	chr1:242465655-242989157	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1014487	chr1:242532959-243011891	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv535367	chr1:242532959-243011891	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv873377	chr1:242607583-243114662	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv998238	chr1:242613214-243041351	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv817408	chr1:242638796-243405454	Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	esv1829728	chr1:242656460-243165286	Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv549466	chr1:242713574-243141099	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv468683	chr1:242739083-243141099	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv549467	chr1:242739083-243141099	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv519429	chr1:242807999-243338216	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv1012007	chr1:242811313-243041351	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv549469	chr1:242842300-243080523	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv470790	chr1:242919915-243309190	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	esv1808313	chr1:242944611-243168762	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	esv1824313	chr1:242945469-243186986	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	esv1848483	chr1:242946450-242988232	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2809879	FH	cis	cerebellum	SCAN
rs2809879	PPPDE1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242945800-242955000	Enhancers	Primary B cells from peripheral blood	blood
2	chr1:242947200-242948600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr1:242947200-242948600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:242947200-242948600	Enhancers	Brain Cingulate Gyrus	brain
5	chr1:242947200-242948600	Enhancers	HSMMtube	muscle
6	chr1:242947200-242948800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:242947400-242948600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:242947400-242948600	Enhancers	Fetal Muscle Leg	muscle
9	chr1:242947600-242948800	Enhancers	HSMM	muscle
10	chr1:242947800-242948600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr1:242948000-242951800	Enhancers	Primary B cells from cord blood	blood
12	chr1:242948200-242948800	Enhancers	Brain Substantia Nigra	brain
13	chr1:242948200-242950800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:242948400-242948800	Enhancers	Brain Hippocampus Middle	brain
15	chr1:242948400-242950600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:242948400-242951800	Weak transcription	Primary hematopoietic stem cells	blood

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